22FD | pdb_000022fd

Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation in complex with NADPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-A0A4Z2CZE1-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295.15	4% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.22	α = 90
b = 86.36	β = 90
c = 183.59	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2023-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97923	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	61.2	100	0.999	16.6	12.8		106193

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95			0.727

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	60.368	106103	5351	99.978	0.192	0.1898	0.1986	0.2273	0.2352	32.766

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.729			-1.15		1.879

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.86
r_dihedral_angle_other_2_deg	12.574
r_dihedral_angle_3_deg	12.386
r_dihedral_angle_2_deg	8.232
r_dihedral_angle_1_deg	6.789
r_lrange_other	6.714
r_lrange_it	6.71
r_scangle_it	5.518
r_scangle_other	5.518
r_scbond_it	3.738
r_scbond_other	3.737
r_mcangle_it	3.606
r_mcangle_other	3.605
r_mcbond_it	2.739
r_mcbond_other	2.739
r_angle_refined_deg	1.532
r_angle_other_deg	0.535
r_symmetry_nbd_refined	0.247
r_nbd_other	0.246
r_nbd_refined	0.217
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.077
r_ncsr_local_group_1	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9050
Nucleic Acid Atoms
Solvent Atoms	539
Heterogen Atoms	182

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing